This directory contains the Feb. 2004 freeze of the Tetraodon 
nigroviridis version 7 (V7) genome assembly (tetNig1) provided by 
Genoscope (http://www.genoscope.cns.fr/). This assembly is the result 
of a collaboration between Genoscope and the Broad Institute of MIT 
and Harvard in Cambridge, MA.

Files included in this directory:

tetNig1.2bit - contains the complete tetraodon/tetNig1 genome sequence
    in the 2bit file format.  While we are providing the .2bit for
    this assembly, we will continue to use the .nib files in
    the Genome Browser.  The utility program, twoBitToFa (available
    from the kent src tree), can be used to extract .fa file(s) from
    this file.  A pre-compiled version of the command line tool can be
    found at:
        http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
    See also:
        http://genome.ucsc.edu/admin/cvs.html
	http://genome.ucsc.edu/admin/jk-install.html

chromAgp.zip - Description of how the assembly was generated,
     unpacking to one file per chromosome.  

chromFa.zip - The assembly sequence in one file per chromosome.
    Repeats from RepeatMasker and Tandem Repeats Finder (with period
    of 12 or less) are shown in lower case; non-repeating sequence is
    shown in upper case.  The main assembly is found in the chrN.fa
    files, where N is the name of the chromosome. The chrN_random.fa
    files contain clones that are not yet finished or cannot be placed
    with certainty at a specific place on the chromosome. In some
    cases, including the human HLA region on chromosome 6, the
    chrN_random.fa files also contain haplotypes that differ from the
    main assembly.

chromFaMasked.zip - The assembly sequence in one file per 
    chromosome. Repeats are masked by capital Ns; non-repeating 
    sequence is shown in upper case.  

chromOut.zip - RepeatMasker .out file for chromosomes. These were 
    created by RepeatMasker at the -s sensitive setting.

chromTrf.zip - Tandem Repeats Finder locations, filtered to keep 
    repeats with period of less than or equal to 12, and translated 
    into one .bed file per chromosome.  

est.fa.gz - Tetraodon ESTs in GenBank. This sequence data is updated 
    once a week via automatic GenBank updates.

md5sum.txt - Checksums for each of the *.zip files.

mrna.fa.gz - Tetraodon mRNA from GenBank. This sequence data is updated 
    once a week via automatic GenBank updates.

xenoMrna.fa.gz - GenBank mRNAs from species other than that of 
    the genome. This sequence data is updated once a week via automatic 
    GenBank updates.


tetNig1.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

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If you plan to download a large file or multiple files from this 
directory, we recommend you use ftp rather than downloading the files 
via our website. To do so, ftp to hgdownload.cse.ucsc.edu, then go to 
the directory goldenPath/tetNig1/bigZips/. To download multiple 
files, use the "mget" command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory) 

All the files in this directory are freely usable for any purpose. 

The Tetraodon sequence has been freely provided by Genoscope before 
publication for use in the UCSC Genome Browser with the following 
understanding: 

1. The data may be freely downloaded, used in analyses, and repackaged 
   in databases. 
2. Users are free to use the data in scientific papers analyzing particular 
   genes and regions, provided that the Genoscope is properly acknowledged.
3. Genoscope reserves the right to publish the initial large-scale analyses 
   of the dataset, including large-scale identification of regions of 
   evolutionary conservation and large-scale genomic assembly. Large-scale 
   refers to regions with size on the order of a Tetraodon chromosome (that 
   is, 5 Mb or more).
4. Any redistribution of the data should carry this notice.
[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt20-Feb-2015 15:32 3.9K 
[TXT]README.txt.bak06-May-2014 16:06 3.8K 
[TXT]md5sum.txt05-May-2014 15:31 418  
[   ]tetNig1.2bit17-Aug-2004 21:10 98M 
[   ]tetNig1.chrom.sizes17-Aug-2004 20:26 422  

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